Indonesia has reiterated that it wants “full transparency” surrounding the naming of President Susilo Bambang Yudhoyono in relation to an Australian court case.

Foreign Affairs Minister Marty Natalegawa said on Tuesday that the President was still waiting for the circumstances of his naming to be made “crystal clear”, suggesting that the Australian government’s response so far has not satisfied him.

The new glitch in relations comes as Dr Natalegawa is trying to negotiate with Australian Foreign Affairs Minister Julie Bishop a code of conduct governing spying between the two countries. He said Australia merely had to agree to Indonesia’s most recent draft, and sign “a commitment not to spy on each other”.

Co-operation between the two countries over anti-people smuggler activities and defence exercises was suspended late last year after the revelation that Australia had spied on the President and his wife. They cannot resume until the countries agree to the code of conduct.

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A blanket suppression order prevents Fairfax Media and other Australian media outlets from reporting the contents of a Victorian Supreme Court case in which Dr Yudhoyono has been named, an affadavit in the case, or even the suppression order itself.

The Department of Foreign Affairs said last week the order was sought to protect the reputation of international leaders from “unwarranted innuendo” emerging from “information that could suggest the involvement in corruption of specific senior political figures in the region, whether in fact they were or not”.

But the tactic backfired badly after the suppression order was leaked to WikiLeaks and published online, forcing Australia to deny that Dr Yudhoyono was a subject of the proceedings involving the former Australian note-printing company Securency.

Asked if he accepted the Australian government response so far, Dr Natalegawa said Indonesia wanted “full transparency [in this case] so as to avoid innuendo and speculation”.

“We want to have this issue to be very clear, crystal clear so to avoid misperception,” he said.

Dr Natalegawa will be meeting Ms Bishop at an ASEAN meeting in Myanmar this weekend, and Dr Yudhoyono has set an August deadline for finalising the agreement between the two countries.

Dr Natalegawa said agreement would be made “as soon as possible”.

“Will it be tomorrow or the day after tomorrow or by the end of the month? It will very much depend on the response of the Australian government over the last draft Indonesia sent to Australia … It is just simple, without revealing the content, at heart it's about a commitment not to spy on each other.”

However, despite the apparently regular speed bumps in the bilateral relationship, Dr Natalegawa said he thought it was “good, going in a positive direction”.

Dr Yudhoyono’s meeting with Prime Minister Tony Abbott on Batam Island in June was “very good, very positive”.

“However, we will continue our efforts to restore the relationship,” the Indonesian foreign minister said.